Origin IGS: aaatatttataaatagcttacttgtattatttataaaaaaatgttaatcttattgtagttatttacaataaaaaagtatttgtgaggagtaacaaattgaatccttttgatatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatatcaaaaggattcaatttgttactcctcacaaatacttttttattgtaaataactacaataagattaacatttttttataaataatacaagtaagctatttataaatattt Mask Tandem Repeat Region ================================================ aaatatttataaatagcttacttgtattatttataaaaaaatgttaatcttattgtagttatttacaataaaaaagtatttgtgaggagtaacaaattgaatccttttgatatt Find is-nt database================================================ Query_seq: TDE1547:TDE1548|TDE1547:TDE1548:ribonuclease HII:conserved hypothetical protein TIGR00103:->->:1591861..1591974 114 aaatatttataaatagcttacttgtattatttataaaaaaatgttaatcttattgtagttatttacaataaaaaagtatttgtgaggagtaacaaattgaatccttttgatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1547:TDE1548|TDE1547:TDE1548:ribonuclease HII:conserved hypothetical protein TIGR00103:->->:1591861..1591974 114 aaatatttataaatagcttacttgtattatttataaaaaaatgttaatcttattgtagttatttacaataaaaaagtatttgtgaggagtaacaaattgaatccttttgatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1547:TDE1548|TDE1547:TDE1548:ribonuclease HII:conserved hypothetical protein TIGR00103:->->:1591861..1591974 114 aaatatttataaatagcttacttgtattatttataaaaaaatgttaatcttattgtagttatttacaataaaaaagtatttgtgaggagtaacaaattgaatccttttgatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatatttataaatagcttacttgtattatttataaaaaaatgttaatcttattgtagttatttacaataaaaaagtatttgtgaggagtaacaaattgaatccttttgatatt Predict ORF larger than 30AA ================================================ aaatatttataaatagcttacttgtattatttataaaaaaatgttaatcttattgtagttatttacaataaaaaagtatttgtgaggagtaacaaattgaatccttttgatatt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaatatttataaatagcttacttgtattatttataaaaaaatgttaatcttattgtagttatttacaataaaaaagtatttgtgaggagtaacaaattgaatccttttgatatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1547:TDE1548|TDE1547:TDE1548:ribonuclease HII:conserved hypothetical protein TIGR00103:->->:1591861..1591974 114 aaatatttataaatagcttacttgtattatttataaaaaaatgttaatcttattgtagttatttacaataaaaaagtatttgtgaggagtaacaaattgaatccttttgatatt Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_002967_TDE1547_TDE1548|ribonuclease HII:conserved hypothetical protein TIGR00103|POSITIVE:POSITIVE|[1591861,1591974]|114 HSP 1 e-value: 4.0E-46 bit: 184.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 aaatatttataaatagcttacttgtattatttatnnnnnnntgttaatcttattgtagttatttacaataaaaaagtatttgtgaggagtaacaaattgaatccttttgatatt aaatatttataaatagcttacttgtattatttataaaaaaatgttaatcttattgtagttatttacaataaaaaagtatttgtgaggagtaacaaattgaatccttttgatatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAUUUAUAAAUAGCUUACUUGUAUUAUUUAUAAAAAAAUGUUAAUCUUAUUGUAGUUAUUUACAAUAAAAAAGUAUUUGUGAGGAGUAACAAAUUGAAUCCUUUUGAUAUU .....((((((((((((......))..))))))))))............(((((((((....)))))))))...((((((...(((((.............)))))..)))))) (-18.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUCAAAAGGAUUCAAUUUGUUACUCCUCACAAAUACUUUUUUAUUGUAAAUAACUACAAUAAGAUUAACAUUUUUUUAUAAAUAAUACAAGUAAGCUAUUUAUAAAUAUUU .................((((((........))))))....((((((((((......))))))))))..........((((((((((............))))))))))..... (-13.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 190 110 79 63 29 NC_002967:TDE2569|5end_3-deoxy-7-phosphoheptulonate_synthase_2596308..2596538_POSITIVE 176 78 41 88 53 NC_002967:TDE0005|5end_L-threonine_aldolase,_low-specificity_6040..6270_NEGATIVE 175 108 74 180 146 NC_002967:TDE2562|5end_cation_ABC_transporter,_permease_protein,_putative_2588899..2589129_POSITIVE 175 90 48 198 147 NC_002967:TDE1575|5end_lipoyl_synthase_1621903..1622133_POSITIVE 175 90 48 95 44 NC_002967:TDE1574|5end_hypothetical_protein_1621800..1622030_POSITIVE 174 57 14 188 145 NC_002967:TDE2509|5end_transcriptional_regulator,_AraC_family_2533188..2533418_POSITIVE 173 57 13 48 2 NC_002967:TDE2330|5end_hypothetical_protein_2366454..2366684_POSITIVE 173 110 81 37 10 NC_002967:TDE1690|5end_hypothetical_protein_1747200..1747430_NEGATIVE 172 104 76 218 197 NC_002967:TDE0783|5end_ribosomal_protein_L18_813520..813750_POSITIVE 168 101 76 74 48 NC_002967:TDE1437|5end_capsular_polysaccharide_biosynthesis_protein_1482232..1482462_POSITIVE 167 90 46 146 97 NC_002967:TDE1314|5end_penicillin-binding_protein_1351174..1351404_POSITIVE 164 109 74 60 23 NC_002967:TDE0990|5end_hypothetical_protein_1017398..1017628_POSITIVE 164 107 72 208 176 NC_002967:TDE0254|5end_hypothetical_protein_288654..288884_POSITIVE 162 31 2 153 120 NC_002967:TDE0812|5end_ABC_transporter,_ATP-binding/permease_protein_832444..832674_POSITIVE 158 90 41 141 90 NC_002967:TDE1170|5end_DNA-binding_protein_1199800..1200030_POSITIVE 157 107 73 68 26 NC_002967:TDE0021|5end_CDP-alcohol_phosphatidyltransferase_family_protein_26814..27044_POSITIVE 156 46 3 124 81 NC_002967:TDE2600|5end_hypothetical_protein_2633958..2634188_POSITIVE 156 89 42 135 81 NC_002967:TDE0722|5end_lipoprotein,_putative_758519..758749_POSITIVE 154 110 75 157 131 NC_002967:TDE1600|5end_ABC_transporter,_ATP-binding/permease_protein_1652396..1652626_NEGATIVE 154 89 42 229 161 NC_002967:TDE1382|5end_transcriptional_regulator,_ArsR_family_1422000..1422230_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 190 110 79 60 26 NC_002967:TDE2568|3end_thiamine_biosynthesis_protein_ThiI_2596385..2596535_POSITIVE 188 44 4 123 74 NC_002967:TDE2017|3end_hypothetical_protein_2039023..2039173_NEGATIVE 187 110 76 138 107 NC_002967:TDE1376|3end_hypothetical_protein_1419079..1419229_POSITIVE 174 66 26 104 62 NC_002967:TDE2023|3end_TPR_domain_protein_2049505..2049655_NEGATIVE 168 101 76 52 26 NC_002967:TDE1436|3end_inner_membrane_protein_1482290..1482440_POSITIVE 162 100 70 98 62 NC_002967:TDE2117|3end_hypothetical_protein_2149175..2149325_POSITIVE 158 106 75 92 61 NC_002967:TDE0494|3end_hypothetical_protein_549559..549709_NEGATIVE 157 107 73 55 13 NC_002967:TDE0020|3end_glycyl-tRNA_synthetase_26881..27031_POSITIVE 155 90 53 113 74 NC_002967:TDE2393|3end_hypothetical_protein_2422588..2422738_POSITIVE 155 88 41 150 105 NC_002967:TDE2214|3end_hypothetical_protein_2253465..2253615_POSITIVE 151 82 41 150 104 NC_002967:TDE1812|3end_hypothetical_protein_1847580..1847730_NEGATIVE 150 60 14 98 45 NC_002967:TDE2768|3end_flagellar_hook_protein_2821119..2821269_NEGATIVE 149 77 41 147 104 NC_002967:TDE1789|3end_hypothetical_protein_1827338..1827488_NEGATIVE 148 88 69 111 92 NC_002967:TDE1015|3end_hypothetical_protein_1045599..1045749_POSITIVE 147 96 52 134 97 NC_002967:TDE0458|3end_hypothetical_protein_514220..514370_POSITIVE 147 96 52 43 6 NC_002967:TDE0457|3end_hypothetical_protein_514129..514279_POSITIVE 146 97 57 135 96 NC_002967:TDE1853|3end_hypothetical_protein_1881966..1882116_NEGATIVE 142 60 12 126 59 NC_002967:TDE0160|3end_hypothetical_protein_187145..187295_NEGATIVE 141 88 41 137 88 NC_002967:TDE1333|3end_hflC_protein,_putative_1370148..1370298_POSITIVE 141 95 66 140 117 NC_002967:TDE0954|3end_branched-chain_amino_acid_ABC_transporter,_permease_protein_978840..978990_POSITIVE